Genomics, Biological Sciences 81.432, University of Massachusetts Lowell
Course SyllabusFor Undergraduates, Fall 2013
Instructor: Dr. Jessica Garb, Assistant Professor, Department of Biological Sciences
Instructor Email: Jessica_Garb@uml.edu Office Hours: Tuesdays 12-2pm Olsen 520
Lecture: T, R 9:30am -10:45pm Room: Olsen 615
Course Description: This three-credit course surveys the field of genomics, examining current technologies and their biological applications. Lectures cover genome organization, genome sequencing and annotation, functional genomics, evolutionary genomics, transcriptomics, proteomics and the role of bioinformatics in organizing and interpreting genomic data.
Course Prerequisites: Genetics 81.235 or Principles of Genetics 81.335
Required Text: Introduction to Genomics by Arthur Lesk, Second Edition, 2012; readings according to schedule below as denoted by asterisk
Additional readings : See attached list, read papers as numbered according to schedule below
(before class), papers posted on course blackboard site
Course Learning Objectives
At the completion of this course:
1. Students will be able to demonstrate an understanding ofgenomes, how they are organized and how genome structure varies across species.
2. Students will be knowledgeable about historical and current methods of whole-genome sequencing and characterization of genome-level expression.
3. Students will be able to explain and utilize basic bioinformatics toolsand databases used in genome annotation and analysis.
4. Students will be conversant in the applications of genomic biology to the fields ofevolutionary biology, medicine, and environmental science.
5. Students will demonstrate improved scientific communication skills through the written exercises, class discussions and debate.
6. Students will become proficient at identifying and interpreting the primary scientific literature related to genomic biology through reading assignment and paper.
Tentative Schedule of Classes
Date Topics and Key Deadlines
R, Sept 5 Course Organization and Introduction to Genomics
Readings
T, Sept 10 Genome content and organization
R, Sept 12 Genome Projects and Bioinformatics
T, Sept17 Applications of Genomics in Biology
*Lesk 1-16
*Lesk 17-35
Lesk, Ch 2
R, Sept 19 Starting a genome project: Mapping and Lesk 80-104 sequencing strategies
T, Sept 24 Next-generation sequencing and genome assembly 1&2)Mardis ‘08, 11
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R, Sept 26
T, Oct 1
R, Oct 3
Genome annotation I: functional genomics
Genome annotation II: junk DNA or not?
! Paper topic due in class or by email!
Exam 1
T, Oct 8 Browsing genomes & other genomic databases
R, Oct 10 Comparative & Evolutionary Genomics
T, Oct 15 Comparative Genomics Continued
! Paper References due in class!
R, Oct 17 Homology, pattern searching & phylogenetics
T, Oct 22 Prokaryotic genomes
3) Temple-Smith et al. 2003
4&5) Warren et al.
2008, Smith 2013
Lesk 104-110
Lesk Ch 4
6)Whittington et al.
2008
Lesk Ch 5
Lesk Ch 6
R, Oct 24 Eukaryotic genomes
T, Oct 29 Human Genome: your genome
R, Oct31 Human Genome Paper discussions & debate
30 minute Review Session
T, Nov 5 Exam II
Lesk Ch 7
Lesk Ch 8
7) Celebration
8) Hall 2010
R, Nov 7 Transcriptomes, microarrays & expression profiling Lesk Ch 9
T, Nov 12 Transcriptomics II: RNA-Seq 9) Wang 2009
! Paper Draft due in class
– bring 2 copies!
R, Nov 14
T, Nov 19
R, Nov 21
Proteomics
Personalized genomics: medical and genealogical application and ethical implications
! Paper Critique due in class
– bring 2 copies!
Systems and network biology: guest lecture
Lesk Ch 10
10) Adey et al.
2013 ; 11) Ferro et al. 2008
Lesk Ch 11
T, Nov 26 Genomic frontiers: Metagenomics & synthetic genomics
12) Turnbaugh et al. 2007; 13)Similie et al. 2011.
R, Nov 28 Thanksgiving holiday
T, Dec 3 Graduate Student Presentations
Course Evaluation
R, Dec 5 Graduate Student Presentations continued;
! Final Papers Due!
Review session TBA Final Exam TBA
Course Assignments:
Exams – Two in-class examinations, and one comprehensive final examination will be given to assess student learning.
Term Paper – Students will write a minimum8page term paper on any topic of their choosing within the field of genomics. The paper will be written in iterative stages, starting with the selection of a topic approved by the instructor (due October 1), the assembly of a list of references (due October 15), a paper draft (due November 12), critique of another student’s
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paper (due November 19) and a final version revised to incorporate comments of the instructor and a student referee (due December 5). More information on the paper will be forthcoming.
Class participation – The class will be small enough to assign periodic student presentations of selected primary articles in the field of genomics. Students will be assessed for their ability to lead, facilitate and contribute to class discussion. Approximately 2 students will lead a short discussion on the assigned primary literature, and prior to the discussion presenters will e-mail
3-4 thought questions to other students (via the instructor) to consider when reading the paper, assignment of the papers will be on a first come basis.
Extra Credit : All students are eligible for extra credit in the form of up to 4 points added to their final grade. For each point you must attend one of the four seminars listed below and submit one page summarizing the seminar talk by the following day in class. Seminars to be held in
Olsen 503 at 4:15pm on Wednesdays
Seminar Speaker Topic
(1) Sept. 25
(1) Oct 9
Dr. Robert Waterhouse, U Geneva/MIT Arthropod Genomics
Dr. Michael Talkowski, Harvard U.
(2) October 23 Dr. Sara Mitchell,
Neurodevelopmental Genomics
Mosquito reproductive genetics
(3) Oct 30
Grading :
Harvard School of Public Health
Dr. Chee-Yeun Chung,
Whitehead Institute
Neuronal regeneration
Examination I 20%
Examination II
Final Exam
Written Paper
20%
20%
25% (topic 1pt, references 4pt, draft 10 pts, final 10pts)
Participation
Total
15% (critique 5 pts, leading & participating in discussion 10 pts)
100%
General Course Policies :

All correspondences to students will be to their student.uml.edu email, so please check your uml student account regularly for updates on changes to the schedule.

Turn cell phones OFF during lectures or the instructor will attempt to answer them.

Using a computer to take notes is acceptable. Using a computer or your cell phone to watch movies, instant message, surf the web, or do other non-course related activities is not appropriate in class.

Please respect the academic code of conduct, see http://www.uml.edu/catalog/undergraduate/policies/academic_dishonesty.htm for the University’s policies on the rules of academic conduct and penalties associated with their violation. Exams and papers are the work of an individual student alone.
Important Dates to Remember:
Last day to add or drop this course: September 17
Withdrawal deadline: November 13
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Tentative Reading schedule (all readings other than Lesk will be posted to blackboard site):
Tuesday, Sept 10 - Introduction to genome content and organization
*Lesk, Ch 1, pages 1-16
Thursday, Sept 12 - Genome Projects and Bioinformatics
*Lesk, Ch 1, pages 17-35
Tuesday, Sept17 - Applications of Genomics in Biology
*Lesk, Chapter 2
Thursday, Sept 19 - Starting a genome project: Mapping and sequencing strategies
*Lesk, Ch 3, pages 80-104
Tuesday, Sept 24 - Next-generation sequencing and genome assembly
1) Mardis, E. 2008. Next-generation DNA sequencing methods. Annual Review of
Genomics and Human Genetics , 9:387-402.
2) Mardis, E. 2011. A decade
’s perspective on DNA sequencing.
Nature 470, 198-203.
Thursday, Sept 26 - Genome annotation I: functional genomics
3) Temple-Smith et al. (2003). A proposal to sequence the genome of the platypus,
Ornithorhynchus anatinus . (Example white paper)
Tuesday, Oct 1 - Genome annotation II: junk DNA or not?
4) Warren et al. 2008. Genome analysis of the platypus reveals unique signatures of evolution. Nature . 453, 175-256. (Example genome paper)
5) Smith. 2013. Death of a genome paper . Frontiers in Genetics . 4, 1-2.
Tuesday, Oct 8 - Browsing genomes & other genomic databases
*Lesk, Ch 3, pages 104-110
Thursday, Oct 10 - Comparative & Evolutionary Genomics
*Lesk, Chapter 4
Tuesday, Oct 15 - Comparative Genomics Continued
6) Whittington et al. 2008. Defensins and the convergent evolution of platypus and reptile venom genes. Genome Research . 18, 986-994.
Thursday, Oct 17 - Homology, pattern searching & phylogenetics
*Lesk, Chapter 5
Tuesday, Oct 22 - Prokaryotic genomes
*Lesk, Chapter 6
Thursday, Oct 24 - Eukaryotic genomes
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*Lesk, Chapter 7
Tuesday, Oct 29 - Human Genome: your genome
*Lesk, Chapter 8
Thursday, Oct 31 - Human Genome Paper discussions & debate
7) A celebration of the genome, Part I. 2011. Science 331, 546-548.
8) Hall, S. 2010. Revolution postponed: the human genome project has been disappointing. Scientific American October 2010, 60-67.
Tuesday, Nov 5- No reading, Exam 2
Thursday, Nov 7 - Transcriptomes, microarrays & expression profiling
*Lesk, Chapter 9
Tuesday, Nov 12 - Transcriptomics II: RNA-Seq
9) Wang et al. 2009. RNA-Seq: a revolutionary tool for transcriptomics. Nature Review
Genetics 10, 57-63.
Thursday, Nov 14
– Proteomics
*Lesk, Chapter 10
Tuesday, Nov 19 - Personalized genomics: medicine, genealogy, & ethics
10) Adey et al. 2013. The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line. Nature500:207-212
11) Feero et al. 2008. The genome gets personal
– almost. JAMA 299, 1351-1352.
Tuesday, Nov 21 - Systems and network biology: guest lecture
*Lesk, Chapter 11
Thursday, Nov 26 - Genomic frontiers: Metagenomics & synthetic genomics
12) Turnbaugh et al. 2007. The human microbiome project. Nature.449: 804-810.
13) Similie et al. 2011. Ecology drives a global network of gene exchange connecting the human microbiome. Nature480 , 241-244.
Tuesday, Dec 3 - No reading, Graduate Student Presentations
Thursday, Dec 5 No reading, Graduate Student Presentations
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